update build.yml

Author: Ziwei-Huang-BU

.github/workflows/build.yml

@@ -1,12 +1,14 @@
 on: [push]
+
 jobs:
   build:
     runs-on: ubuntu-latest
     permissions:
       contents: write
     container: bioconductor/bioconductor_docker:devel
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Query dependencies
         run: |
@@ -16,22 +18,24 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: /usr/local/lib/R/site-library
+          # bump the prefix if you need to bust the cache
           key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-1-
 
       # This lets us augment with additional dependencies
       # - name: Install system dependencies
-      #  if: runner.os == 'Linux'
-      #  env:
-      #    RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-      #    GITHUB_PAT: ${{ secrets.OMICSIGNATURE_TOKEN }}
-      #  run: |
-      #    Rscript -e "remotes::install_github('r-hub/sysreqs')"
-      #    sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-      #    sudo -s eval "$sysreqs"
+      #   if: runner.os == 'Linux'
+      #   env:
+      #     RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+      #     GITHUB_PAT: ${{ secrets.OMICSIGNATURE_TOKEN }}
+      #   run: |
+      #     Rscript -e "remotes::install_github('r-hub/sysreqs')"
+      #     sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+      #     sudo -s eval "$sysreqs"
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
@@ -45,22 +49,24 @@ jobs:
         shell: Rscript {0}
 
       # Push docker image to docker hub
-      #- uses: docker/build-push-action@v1
-      #  with:
-      #    username: ${{ secrets.DOCKER_USERNAME }}
-      #    password: ${{ secrets.DOCKER_PASSWORD }}
-      #    repository: montilab/rpkgs
-      #    tag_with_ref: true
-      #    tag_with_sha: true
-      #    tags: latest
+      # - uses: docker/build-push-action@v1
+      #   with:
+      #     username: ${{ secrets.DOCKER_USERNAME }}
+      #     password: ${{ secrets.DOCKER_PASSWORD }}
+      #     repository: montilab/rpkgs
+      #     tag_with_ref: true
+      #     tag_with_sha: true
+      #     tags: latest
 
       - name: DevTest
         run: |
-           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site("."); file.copy("README_files", "docs", recursive=TRUE)'
+          PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site("."); file.copy("README_files", "docs", recursive=TRUE)'
+
       - name: Install deploy dependencies
         run: |
           apt-get update
           apt-get -y install rsync
+
       - name: Deploy 🚀
         uses: JamesIves/github-pages-deploy-action@v4
         with: